Commit 16931433 authored by Andrey Filippov's avatar Andrey Filippov
Browse files

bug fixes, NaNs in eigen, blanking individual tiles with fpn

parent 388be26d

src/main/java/com/elphel/imagej/tileprocessor/Correlation2d.java

+28 −8
Original line number Diff line number Diff line
@@ -2753,15 +2753,21 @@ public class Correlation2d { 
		}

		x0 += sx / s0; // relative to top-left

		y0 += sy / s0;

		

		//https://users.cs.utah.edu/~tch/CS4640/resources/A%20geometric%20interpretation%20of%20the%20covariance%20matrix.pdf

		double cxx = sx2 - sx * sx / s0, cyy= sy2 - sy * sy / s0, cxy = sxy - sx * sy / s0;

		if ((sx2 == 0) ||(sy2 == 0) || (cxx == 0) || (cyy == 0)){

			return null;

		}

		

		double [][] acovar =  {{cxx, cxy},{cxy,cyy}};

		// TODO: calculate for 2x2 faster?

		double [] xy = {x0-center_xy, y0-center_xy}; // relative to the center

		double [] rslt;

		if (eig_fast2x2) {

			double [] eig = getEigen2x2(acovar);

			if (eig == null) {

				return null;

			}

			rslt = new double[] {

					xy[0], // x0 - center_xy,

					xy[1], // y0 - center_xy,
@@ -2787,13 +2793,19 @@ public class Correlation2d { 
					eigval[1-eig_indx]};

			if (debug){

				 double [] r = getEigen2x2(acovar);

 				 if (r!= null) {

 					 System.out.println(String.format("%10f %10f", rslt[3], r[0])); 

 					 System.out.println(String.format("%10f %10f", rslt[4], r[1])); 

 					 System.out.println(String.format("%10f %10f", rslt[5], r[2])); 

 					 System.out.println(String.format("%10f %10f", rslt[6], r[3]));

 				 } else {

 					 System.out.println("Got null from getEigen2x2()"); 

 				 }

			}

		

		}

		if (Double.isNaN(rslt[3])) {

			System.out.println("getMaxXYCmEig(): Got NaN");

		}

		

		if (debug){

			System.out.println("getMaxXYCm() -> "+rslt[0]+":"+rslt[1]+" ("+rslt[2]+
@@ -2882,10 +2894,18 @@ public class Correlation2d { 
		}

		double [] lambda = {hapd-d, hapd+d};

		double [] v0 = {A[0][0] - lambda[1], A[1][0]};

		double  k = 1.0/Math.sqrt(v0[0]*v0[0] + v0[1]*v0[1]);

		double l = Math.sqrt(v0[0]*v0[0] + v0[1]*v0[1]);

		if (l==0) {

			return null;

		}

		double  k = 1.0/l;

		if (v0[0] < 0) { // to be compatible with standard?

			k = -k;

		}

		if (Double.isNaN(k) || Double.isNaN(v0[0])) {

			System.out.println("getEigen2x2(): Got NaN");

		}



		return new double [] {k*v0[0], k*v0[1], lambda[0], lambda[1]};

	}

src/main/java/com/elphel/imagej/tileprocessor/Interscene.java

+53 −6
Original line number Diff line number Diff line
@@ -3841,6 +3841,7 @@ public class Interscene { 


	    boolean fpn_remove =           !fpn_disable && clt_parameters.imp.fpn_remove;

	    double  fpn_max_offset =       clt_parameters.imp.fpn_max_offset;

	    final double  fpn_min_offset = clt_parameters.imp.fpn_min_offset;

	    double  fpn_radius =           clt_parameters.imp.fpn_radius;

	    boolean fpn_ignore_border =    clt_parameters.imp.fpn_ignore_border; // only if fpn_mask != null - ignore tile if maximum touches fpn_mask

	    boolean show_tptask_ref =      false;
@@ -4193,16 +4194,14 @@ public class Interscene { 
			}

		}



		double [][] fpn_offsets = null;

		if (fpn_remove) {

			fpn_offsets = getInterCorrOffsets(

		final double [][] fpn_offsets = fpn_remove ?  getInterCorrOffsets(

					fpn_max_offset, // final double   max_offset,

					tp_tasks_ref,   // final TpTask[] tp_tasks_ref,

					tp_tasks[0],       // final TpTask[] tp_tasks,

					first_scene.getNumSensors(), // final int      numSens,

					tilesX,         // final int      tilesX,

					tilesY);        // final int      tilesY);

		}

					tilesY) : null;        // final int      tilesY);

		

		// Verify offsets before running LMA, return null and reason if test fails.

		if (min_max != null) {

			double [][] offsets = getInterCorrOffsets(
@@ -4438,8 +4437,20 @@ public class Interscene { 
				}

				return null;

			}

			

		}

		int nremoved = 0;

		if ((fpn_offsets != null) && (fpn_min_offset > 0)) {

			nremoved = removeFPNTiles(

					fpn_offsets,     // final double [][]   fpn_offsets,

					fpn_min_offset,  // final double        fpn_min_offset,

					coord_motion,    // final double [][][] coord_motion,

					1); // final int           offset_index)

			if (debug_level > -3) {

				System.out.println("Removed "+nremoved+

						" tiles as their peaks are too close to the FPN predicted offset (<"+fpn_min_offset+"pix");

			}

		}

		

		// optional coord_motion[1][3..4] is reserved for disparity difference and strength

		// final int                 globalDebugLevel);

		if (use3D) {//(scene_disparity_strength != null)
@@ -4823,6 +4834,42 @@ public class Interscene { 
		return null;

	}

	

	public static int removeFPNTiles(

			final double [][]   fpn_offsets,

			final double        fpn_min_offset,

			final double [][][] coord_motion,

			final int           offset_index) {

		if (fpn_offsets == null) {

			return 0;

		}

		final double fpn_min_offset2 = fpn_min_offset * fpn_min_offset;

		final Thread[] threads = ImageDtt.newThreadArray(THREADS_MAX);

		final AtomicInteger ai =        new AtomicInteger(0);

		final AtomicInteger anremoved = new AtomicInteger(0);

		for (int ithread = 0; ithread < threads.length; ithread++) {

			threads[ithread] = new Thread() {

				public void run() {

					for (int nTile = ai.getAndIncrement(); nTile < fpn_offsets.length; nTile = ai.getAndIncrement()) {

						if ((fpn_offsets[nTile] != null) && (coord_motion[offset_index][nTile] != null)) {

							double dx = coord_motion[offset_index][nTile][0] - fpn_offsets[nTile][0];

							double dy = coord_motion[offset_index][nTile][1] - fpn_offsets[nTile][1];

							double l2 = dx*dx + dy*dy;

							if (l2 < fpn_min_offset2) {

								for (int i = 0; i < coord_motion.length; i++) {

									coord_motion[i][nTile] = null;

								}

								anremoved.getAndIncrement();

							}

						}

					}

				}

			};

		}		      

		ImageDtt.startAndJoin(threads);

		return anremoved.get();

		

	}



	

	public static boolean [] getMovementMask(

			CLTParameters clt_parameters,

src/main/java/com/elphel/imagej/tileprocessor/IntersceneLma.java

+22 −7
Original line number Diff line number Diff line
@@ -806,7 +806,7 @@ public class IntersceneLma { 
		if (eigen == null) {

			return null;

		}

		final double [][][] transform = new double[eigen.length][2][2];

		final double [][][] transform = new double[eigen.length][][];

		final Thread[] threads = ImageDtt.newThreadArray(QuadCLT.THREADS_MAX);

		final AtomicInteger ai = new AtomicInteger(0);

		final double k0 = 1.0/eig_max_sqrt;
@@ -816,6 +816,8 @@ public class IntersceneLma { 
				public void run() {

					for (int iTile = ai.getAndIncrement(); iTile < eigen.length; iTile = ai.getAndIncrement()) if (eigen[iTile] != null){

						double [][] am = {{eigen[iTile][0],eigen[iTile][1]},{eigen[iTile][1],-eigen[iTile][0]}};

						if (!Double.isNaN(am[0][0]) && !Double.isNaN(am[0][1])) {

							transform[iTile] = new double [2][2];

							for (int i = 0; i < 2; i++) {

								double k = Math.max(0, 1/Math.max(eig_min_sqrt, Math.sqrt(eigen[iTile][2+i]))-k0);

								for (int j = 0; j < 2; j++) {
@@ -824,6 +826,7 @@ public class IntersceneLma { 
							}

						}

					}

				}

			};

		}		      

		ImageDtt.startAndJoin(threads);
@@ -849,8 +852,13 @@ public class IntersceneLma { 
					int thread_num = ati.getAndIncrement();

					for (int iMTile = ai.getAndIncrement(); iMTile < vector_XYSDS.length; iMTile = ai.getAndIncrement()) if (vector_XYSDS[iMTile] != null){

						double w = vector_XYSDS[iMTile][2];

						if ((eig_trans != null) && (eig_trans[iMTile] == null)) {

							w = 0;

							continue;

						}

						if (Double.isNaN(w)) {

							w = 0;

							continue;

						}

						if (w > 0) {

							anum_defined.getAndIncrement();
@@ -1069,6 +1077,9 @@ public class IntersceneLma { 
												jt[i][num_components * iMTile + 2] = deriv_params[indx][2]; // pY (disparity is used)

											}

										}

										if (Double.isNaN(jt[0][num_components * iMTile + 0])) {

											System.out.println("getFxDerivs(): NaN, iMTile="+iMTile);

										}

									}

								}

							} else if (mb_mode) {
@@ -1123,9 +1134,13 @@ public class IntersceneLma { 
							double d = 0.0;

							for (int k = 0; k < nup_points; k++) {

								if (jt[i][k] != 0) {

									d+=0;

									d+=0; // ???

								}

								d += weights[k]*jt[i][k]*jt[j][k];

								if (Double.isNaN(d)) {

									System.out.println("getWJtJlambda(): NAN i="+i+", j="+j+", k="+k);

								}

								

							}

							wjtjl[i][j] = d;

							if (i == j) {

src/main/java/com/elphel/imagej/tileprocessor/IntersceneMatchParameters.java

+7 −0
Original line number Diff line number Diff line
@@ -509,6 +509,7 @@ min_str_neib_fpn 0.35 
	// Remove correlation caused by FPN

	public  boolean fpn_remove =                    true;  // only use reference DSI tiles that have LMA (strong) disparity

	public  double  fpn_max_offset =                8.0;   // pix - ignore larger FPN offsets

	public  double  fpn_min_offset =                1.8;   // pix - ignore tile if maximum differs less from fpn offset 

	public  double  fpn_radius =                    0.75;  // pix - zero around center 

	public  boolean fpn_ignore_border =             false; // only if fpn_mask != null - ignore tile if maximum touches fpn_mask
@@ -1461,6 +1462,8 @@ min_str_neib_fpn 0.35 
				"Zero-out integrated inter-scene correlation around zero-shift offset");

		gd.addNumericField("Maximal FPN offset to consider",         this.fpn_max_offset, 6,7,"pix",

				"Maximal offset from the zero shift to consider (normally just 8 pix)");

		gd.addNumericField("Closest peak from the FPN offset",       this.fpn_min_offset, 6,7,"pix",

				"Discard tile if maximum is closer to the fpn offset");

		gd.addNumericField("FPN suppression radius",                 this.fpn_radius, 6,7,"pix",

				"Blank correlation pixels closer than this distance from the FPN offset");

		gd.addCheckbox ("Ignore maximums \"touching\" FPN",          this.fpn_ignore_border,
@@ -2119,6 +2122,7 @@ min_str_neib_fpn 0.35 
		this.use_lma_dsi =              gd.getNextBoolean();

		this.fpn_remove =               gd.getNextBoolean();

		this.fpn_max_offset =           gd.getNextNumber();

		this.fpn_min_offset =           gd.getNextNumber();

		this.fpn_radius =               gd.getNextNumber();

		this.fpn_ignore_border =        gd.getNextBoolean();
@@ -2691,6 +2695,7 @@ min_str_neib_fpn 0.35 
		properties.setProperty(prefix+"use_lma_dsi",          this.use_lma_dsi+"");         // boolean

		properties.setProperty(prefix+"fpn_remove",           this.fpn_remove+"");          // boolean

		properties.setProperty(prefix+"fpn_max_offset",       this.fpn_max_offset+"");      // double

		properties.setProperty(prefix+"fpn_min_offset",       this.fpn_min_offset+"");      // double

		properties.setProperty(prefix+"fpn_radius",           this.fpn_radius+"");          // double

		properties.setProperty(prefix+"fpn_ignore_border",    this.fpn_ignore_border+"");   // boolean
@@ -3221,6 +3226,7 @@ min_str_neib_fpn 0.35 
		if (properties.getProperty(prefix+"use_lma_dsi")!=null)          this.use_lma_dsi=Boolean.parseBoolean(properties.getProperty(prefix+"use_lma_dsi"));

		if (properties.getProperty(prefix+"fpn_remove")!=null)           this.fpn_remove=Boolean.parseBoolean(properties.getProperty(prefix+"fpn_remove"));

		if (properties.getProperty(prefix+"fpn_max_offset")!=null)       this.fpn_max_offset=Double.parseDouble(properties.getProperty(prefix+"fpn_max_offset"));

		if (properties.getProperty(prefix+"fpn_min_offset")!=null)       this.fpn_min_offset=Double.parseDouble(properties.getProperty(prefix+"fpn_min_offset"));

		if (properties.getProperty(prefix+"fpn_radius")!=null)           this.fpn_radius=Double.parseDouble(properties.getProperty(prefix+"fpn_radius"));

		if (properties.getProperty(prefix+"fpn_ignore_border")!=null)    this.fpn_ignore_border=Boolean.parseBoolean(properties.getProperty(prefix+"fpn_ignore_border"));
@@ -3759,6 +3765,7 @@ min_str_neib_fpn 0.35 
		imp.use_lma_dsi           = this.use_lma_dsi;

		imp.fpn_remove            = this.fpn_remove;

		imp.fpn_max_offset        = this.fpn_max_offset;

		imp.fpn_min_offset        = this.fpn_min_offset;

		imp.fpn_radius            = this.fpn_radius;

		imp.fpn_ignore_border     = this.fpn_ignore_border;

src/main/java/com/elphel/imagej/tileprocessor/OpticalFlow.java

+12 −1
Original line number Diff line number Diff line
@@ -6492,19 +6492,30 @@ public class OpticalFlow { 
			start_ref_pointers[0] = earliest_scene;

			start_ref_pointers[1] = ref_index;

		}

		String top_dir = quadCLTs[ref_index].getX3dTopDirectory();

		// temporary fix save/restore linkedModels, sourceDirectory, sourcePaths

		// that are copied main-> aux in EyesisCorrectionParameters.updateAuxFromMain()

		// quadCLT_main.correctionsParameters

		String bkp_linkedModels = quadCLT_main.correctionsParameters.linkedModels;

		String bkp_videoDirectory = quadCLT_main.correctionsParameters.videoDirectory;

		String bkp_x3dDirectory = quadCLT_main.correctionsParameters.x3dDirectory;

		String bkp_mlDirectory = quadCLT_main.correctionsParameters.mlDirectory;

		String bkp_sourceDirectory =  quadCLT_main.correctionsParameters.sourceDirectory;

		String [] bkp_sourcePaths =   quadCLT_main.correctionsParameters.sourcePaths;

		boolean bkp_use_set_dirs = quadCLT_main.correctionsParameters.use_set_dirs;

		quadCLTs[ref_index].saveConfInModelDirectory(); // save all (global) configurations in model/version directory

		quadCLT_main.correctionsParameters.linkedModels =    bkp_linkedModels;

		quadCLT_main.correctionsParameters.videoDirectory = bkp_videoDirectory;

		quadCLT_main.correctionsParameters.x3dDirectory = bkp_x3dDirectory;

		quadCLT_main.correctionsParameters.mlDirectory = bkp_mlDirectory;

		quadCLT_main.correctionsParameters.sourceDirectory = bkp_sourceDirectory;

		quadCLT_main.correctionsParameters.sourceDirectory = bkp_sourceDirectory;

		quadCLT_main.correctionsParameters.sourcePaths =     bkp_sourcePaths;

		quadCLT_main.correctionsParameters.use_set_dirs =    bkp_use_set_dirs;

		

		System.out.println("buildSeries(): DONE"); //

		return quadCLTs[ref_index].getX3dTopDirectory();

		String top_dir0=quadCLTs[ref_index].getX3dTopDirectory();

		return quadCLTs[ref_index].getX3dTopDirectory(); // top_dir; // 

    }

    

	public void adjustLYSeries(